Phantom Project
by Just a Happy Wombat
Summary: Years passed after the events of Scorpia Rising, but right before Alex gets close enough to believe that he can live a normal, ordinary life, the shadows of his past return and push him back to the world of espionage one last time. Sabina is kidnapped and Alex's only chance is to team up with one of his greatest enemies to save her... and to save the world.
1. Chapter 1

**Hi everyone! This is my really first Alex Rider themed fanfic, I hope you will like it!**

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 **Disclaimer: I do not own the Alex Rider series**

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 ** _Phantom Project_**

 _Chapter 1_

Three entrances, windows that are low enough to jump through: multiple escape opportunities. _Check._  
Children, the same age as you are: camouflage. _Check._  
Pens: equipment that can be somehow turned to weapons if needed. _Check.  
_ Suspicious people: possible enemies. _Searching..._

Although he'd been living in America for years, Alex Rider still couldn't get used to the new environment. After all he'd gone through, he couldn't feel safe anywhere anymore.

"Hey, what's your last lesson?" Sabina Pleasure was walking next to him on the corridor.  
Alex looked dizzily at her, such as she'd woke him up from a long dream. "P.E."  
"Right." The girl said. "Then we can meet in front of the gym after that and get home together."  
Alex noded and turned to the right wing of the building. Sabina went to the other direction.

Then, he could hear the bell go off. He had to run to avoid getting late.  
On the way, he saw workers dressed in orange jumpsuits. They were swapping the light bulbs of a classroom. As he ran past them, one of the men stood in front of him, blocking his way. He tried to get past, but then he saw a shiny little object in his right hand. A gun.

"Come with me, kid, I've got a friend who wants to have a nice chat with you!" He smiled, getting closer and closer to the boy. Alex took a step back. He was wondering about performing a karate kick, but it was too risky. He was in point blank range and concluding from the other mechanics' reaction – who didn't even bat an eye – Alex was sure that they were with the attacker. In this situation, all he could do was obeying.

The man led him through endless corridors, but stopped at the canteen. It was about 14:00 and most of the children were having lunch there.  
"If you say a word..." The man whispered to his ears, pushing the barrel to Alex's back.

They went next to tables with youngsters waving to Alex, greeting him. He tried to alert them, but they didn't get it. Finally, he peeked around the area to find something useful. _Nothing._

Then, they got into the kitchen. The air was hot by the ovens. To Alex's surprise, there was noone around, so he was left alone with the man surrounded by huge pots, frying pans and pieces of cutlery.

When they stopped, Alex finally had time to examine the other one's face. He looked somehow familiar to him, but he had no clue from where. There was only one thing obvious: he was there for no good.

The man in the orange jumpsuit smiled at him. "It's good to see you again, Rider, but I am afraid, it will be the last time."

The boy moved backwards as he saw the assassin rise the gun, making it ready to be shot.  
 _Then, he pulled the trigger._

Everything happened so fast, that the adult couldn't even comprehense it.  
In a split second, Alex took the top of a giantic pot and pushed himself to the floor, throwing the metal object at the man the same time.

The bullet missed its aim, making a mark on the wooden surface of a counter. Alex was all right, but he couldn't say the same about his attacker. The assassin was laying unconscious on the floor.

However, he had no time to relax: the shot was so loud, that it could be heard anywhere inside the building for sure. And it was the last thing Alex needed to be seen by the students and teachers flooding into the room. _No._ He ended his spy career and didn't want to start the long line of interrogations and returning memories again. _Just no._

He saw a window with the view of the schoolyard and rushed to it. To his luck, it wasn't closed.  
He opened it, glancing out. He was about four metres above the ground.

Then, he heard footsteps. " You!" Someone shouted from the behind.

 _"I won't get back to that hell with MI6. No, no and no!"_ He thought and made up his mind.  
Alex climbed up to the frame of the window and jumped.

Fortunately, the enormous shurb under the window saved his life. Anyway, it could have made him happier, if it had had no thorns.

Children gathered around him after they saw him fall, but he didn't care. He stood up and began to run and get himself free from the branches and leaves sticked to his clothes on the way.

He knew that the man wasn't alone. There were about three other orange-jumpsuited goons.  
Alex could only think of one person. Sabina.

He remembered that the girl had chemistry lesson that time and started heading to the laboratory. He had to take her to safety.

When he entered the building again, a guy in a white cloak ran up to him. His name was Kevin and he visited the same lesson as Sabina.  
"Get away, Rider!" He shouted at him while rushing to the main exit. "There must be some kind of terrorist attack here."  
"Where's Sabina?" Alex asked, but the boy was already far away from him.

Alex ran to the lab so fast that he could feel terrible pain in his legs.  
The room had two huge white doors, which were originally closed, but this time, they were wide open.  
When he entered, he saw broken test tubes everywhere and some unknown liquid dripping from a desk to the ground. The sound it made drove Alex crazy.

 _"Here must have been a fight."_ He thought, seeking even more desperately for the girl.  
He wanted to push his fists to the wall. _Nothing._ Sabina was gone, hell knows where.

 _"Maybe she went home with the others."_ He thought, but it seemed too unbelivable for him. The girl would never leave him behind this way for sure.

Then, his eyes stopped on the board. It wasn't a chemical reaction written on it, but a short, three-word sentence that sent shivers down his spine.

 ** _Scorpia never forgets._**

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 **This is the end of Chapter 1.**

 **If you like it, drop me a review, please - that would mean a lot to me. :)**


	2. Chapter 2

**I'm back!**

 **To start with, thank you for the favs/follows- it's the most motivating thing ever! :D**

 **Also, a big thanks goes for the review to Platero. To answer your question, Alex is 17.  
About his relationship with Sabina: they are rather like bf/gf, but not offically... _not yet..._ :)**

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 _Chapter 2_

 _Faster...Faster...FASTER!_

 _"I have to warn Mr. and Mrs. Pleasure!"_ Alex thought as he produced his phone from his pocket on the way, but as he wanted to turn it on, the little gadget started beeping and the screen went black. The battery was off.

 _Faster...Faster...FASTER!_

Cars tooted all around him as he zigzaged between them.  
"Are you insane?" A man asked, nearly crashing his truck with him.

 _Faster...Faster...FASTER!_

Alex had never pedalled with such speed before. He had taken a bike on the way out of school.  
He knew that Mrs. Pleasure had a day off, so he had to get home to her before Scorpia did.

 _Faster...Faster...FASTER!_

In front of him, cars were bumper to bumper. Traffic jam. So close to his aim, but still...  
 _Not now...  
_ He was stuck between a van and a bus, no place to get away.

A new lane was built, waiting to be opened.

Alex swore, getting off the bike, but then the sound of the horns got louder. And no, it wasn't him, who made the crowd indignant.  
A huge black jeep with darkened windows was heading to his direction next to the traffic, using the new part of the road. From the window, Alex saw a man with sunglasses, dressed in an orange jumpsuit.  
One of the fake mechanics.

 _"Sabina must be there with him."_

Alex knew that it was a crazy idea. Maybe the craziest one he'd ever made up.  
Still, he had no chance to contemplate it.

He acted without thinking. He threw the bycicle away and climbed to the top of the van next to him.

 _"It's all about timing. If it's OK, then maybe..."_

The jeep was getting extremely close to him. He knew what to do. There was no way back – not after that he made his decision.

He was high up on the vechile with people looking at him from every direction. If he jumped in the wrong moment or fell, he would die for sure.

Alex closed his eyes, starting a countdown.

3

2

1

JUMP!

...

Alex hit the top of the jeep hard and nearly rolled off it, but in the last second, he could catch a hold.

However, it was by far not the worst part.

The driver stepped on the accelerator with all his strength, making the fresh asphalt flame under them.

Alex slipped backwards, losing his balance and control. Then, his hands left the roof.

"No!" The boy shouted, but before he could crash to the solid ground, he grabbed his belt.

"One last chance..." He thought desperately, pressing a little button on it.

Smithers' goodbye-present came handy –as always.  
The metal part of the belt opened up, shooting a little iron arrow to the back of the jeep. It was connected with an amazingly thin and strong thread to Alex's belt.

And the consequence?

The boy was pulled after the rushing vechile, which was taking a right turn to a little, empty street.  
Luckily, he wasn't smashed to anything. But he had no time to relax.

Suddenly, the jeep stopped, sending Alex fly above it. Finally, his body was pushed to a wall, ricocheting to the cold concrete pavement – right before the car.

He wanted to stand up, but the pain in his legs was too much and with a groan, he fell back.  
All he could do was glancing into the yellowish lights of the jeep.

He was getting ready to be hit by the bumper, but then the door of it opened and an assassin got out, bringing a bright object in his hands. _Sabina's bag._  
Then, he threw it to him cruelly.  
"A last gift from your girlfriend." He smiled.

Meanwhile, the jeep left, turning back to the main street. To the Pleasure's house.

Alex's eyes looked into the ones of the man, then met the barrel of a pistol.  
"My colleague could aim in a terrible way, but I can assure you that I'm a pro." He said.

"However, you are still unable do your job properly..." Said a third person, stepping out of the shadows.  
"... Just like our young friend. Right, Alex?" The man asked mockingly.  
He was wearing dark coloured jeans with a black coat, which – with the light falling on him - made his skin look paler, like a ghost's.

There was only one thing that couldn't fit into the image: no ghost has any scar along his neck.

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 **Thanks for reading!**


	3. Chapter 3

**Here is the next chapter, R &R please! :)**

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Chapter 3

When Alex opened his eyes, the first thing he saw was a photo of himself with the Pleasures. It was taken on the day he arrived to the USA with them to start a new life.

As he looked around, he realised that he was sitting in his own room on his own bed – at home.

 _"What if it was just a dream?"_ He asked himself. The thought mixed with hope filled his mind so fast that it made him dizzy.  
What if the whole thing was a nightmare and when he got out the room, he would hear Mr. Pleasure watching a football match in the living room, inviting him to join in? What if he could see Mrs. Pleasure cooking something delicious if he entered the kitchen? What if he opened the door of his room and came across Sabina smiling at him, making a joke of the confused expression he might have had on his face that time, laughing at him, safe and sound?

Alex stood up, heading to the door, paying no attention to the pain somewhere near his ribs. He didn't care where it came from or what caused it - he was unable to believe that the attack on him and his family was not a result of his imagination. Just not.

He pressed down the handle.

When the door opened, the sudden light coming from the corridor blindened him. After his eyes finally got used to the daylight coming from the huge windows of the living room, he started checking around.

The first place he went to was Sabina's room. It looked like being after a cyclone – the same way it always did when she overslept and was running to catch the school bus.  
Alex peered at her desk. The books she was learning from last night were lieing on it. The boy touched one of them with his index finger, shimmering the dog-eared pages.

They made his fingers back - there was a huge layer of dust on them.

Alex's eyes widened. That could have been anything, but a good sign.

Suddenly, he noticed voices coming from the room next to Sabina's.  
Someone else was in the building.

He pushed himself to the wall, trying to catch a word, but he was unable to understand anything.  
He sneaked out to the corridor to hear it better.

"...If they are after them... We have the bait, they would come for it..." A man – who wasn't Mr. Pleasure for sure - said, but stopped. The unexpected silence put Alex on high alert, but before he could have got away, the door opened.

"Ah, Alex, has noone told you that it's not good manners harkening?" Yassen Gregorich asked. He was wearing the same outfit when Alex saw him last time – speaking to the man pointing a gun to Alex's forehead before he passed out.

"Impossible! I saw you die!" The boy shouted, getting to fighting position, but the pain reappeared into his chest, making him groan.

"Well, as you can see now, I am more alive than ever... something that couldn't have been said about you two days ago." Yassen said.

"Two days?" Alex shook his head with disbelief. It was just getting too much for him. Sabina was gone and to make matters worse, his greatest enemy, the man who killed his uncle was alive.  
He swallowed. Enemy or not, Yassen was possibly the only one who could answer his questions.

"Sabina," He started. "she got kidnapped, right?"

Yassen gave him a quick nod.

"But I am not." Alex continued. "And I wasn't shot either, although the man there really got me. Why?"

"I've got plans including you." Yassen cut it short.

Alex felt like becoming more and more fed up with the man. He not only gave no information away, but also talked about the events with such annoyance, that it infuriated Alex enough to... To what? He was injured, facing an armed, well trained assassin. With these conditions, he couldn't be a match for Yassen.

"What plans?" He finally asked.

"You'll see." The man replied. "Right now, all you have to do is obeying my orders."

Alex's shook his head. "Obey? No way!"

"Then, what will you do?" Yassen asked mockingly. "Run to dear MI6 and get yourself killed?"

"Even MI6 is better than you." Alex said and he meant it.

"Not with Scorpia controlling it." The assassin replied, making the eyes of the boy wider. Then, without waiting for the shocked Alex to ask the question that was still hanging in the air, he led him into the room and gave him a sheet of paper.

"This is an immediate attack order sent to every active MI6 agent in this region, describing your location." Yassen explained. "I guess, you would like to see who signed it."

 _Tulip Jones, Head of Special Operations._

Alex read it out with disbelief. "No! It's impossible! Mrs. Jones would never do so."

"She would, if she had no other choice, Alex." Yassen said. "Scorpia is out for revenge, but this time, they have chosen another tactic. Although I do not have enough information to fully confirm it, but it seems that they succeeded putting some of their own agents into really influential positions in the British government. "

"So... that means that..."

"That means, that they can order MI6 around, just the way they like it." Yassen pointed out. "And they are controling the other secret services the same way."

"However, we still have numerous reasons to suppose, that this is only the first step of their plan called the Phantom Project. Now, everyone is to eliminate all the endangering factors – which includes you..." Yassen stopped for a moment to let Alex comprehense each word.

"But what do they want?" Alex asked. "And why don't you fight on their side?"

"Scorpia never forgets and never forgives." Yassen said monotonously as if he was telling a short text he had to learn by heart. "After the events with Cray, I went into hiding. I had enough money to live a good life, so I wanted to quit. However, they found it out and sent their henchmen after me. And no, if I brought you to them, they would kill me the same way. This is how Scorpia works."

"But..."

"With MI6 and the others on their side, our only chance is an alliance – a truce to be more precise."

Alex wanted to say something, but a round-shape, dark object thrown through the window took his attention. Yassen noticed it too, then pushed the boy to the floor, right before it blew up, sending a huge smoke of poison gas into the air.


	4. Chapter 4

**Hi! Sorry for not updating for while!**

 **Here's Chapter 4, I hope you will like it:**

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 _Chapter 4_

The gas bomb exploded only a little distance away from their heads.

Alex'd fallen onto his arms, that were still aching from the force, and from the venomous smoke, his senses went numb. His vision was getting obscure, all he could see was dust and darkness. He knew that he had to get oxygen soon, or he would be dead in no time.

He tried to stand up, but changed his mind extremely fast: although his ears were tingling, he could still hear the repetitive sound of gunshots.  
Finally, he started to crawl on the cold floor to the direction of the back door of the house, but a strong fist grabbed his T-shirt.

"Alex!" Yassen was next to him, wiping blood from his face. The boy stopped.

New voices came from the outside from a loudspeaker.

"We know you are inside!" A policeman shouted. "Come out with your hands up or we'll go inside!"

The gaze of Alex met Yassen's. The man was signing with his hands, but Alex couldn't understand it.  
Then, Yassen started moving towards the stairs. The boy followed him.

"Last warning!" The officer shouted. "You've got 10 seconds until we break in the door."

As they tried to get past the derbis left after the explosion, Alex's knee started to feel worse and worse. He didn't know if the fall or the encounter with the kidnapers was responsible for it, but there was one thing for sure: from step to step, the pain returned with newer strenght, sending stars circle in his vision.

Yassen, on the other hand was quite ok, if his head injury didn't count. The boy had no idea where the man was heading to, but following him was his only chance to survive.

Alex had no clue how many seconds had passed when they arrived to the attic, but he was sure that the deadline had expired. As an evidence, he could hear the commando rush through the rooms underneath.

 _"Poor Mr. and Mrs. Pleasure,"_ He muttered to himself. _"I've ruined everything!"_

He looked at Yassen who stood up, ready to climb to the roof.

"What are you doing?" Alex asked, but no answer came, just a short _"Come!"_

Then, he heard the sound of the spinning blades of a helicopter. It was metres above them with a ladder made of rope falling down for them.

The policemen saw it too, and started to open a fire on it.  
Yassen was the first to go. He climbed up with an amazing agility and finished unharmed in his seat.

Alex looked up, contemplating his position.  
There were bullets racing from the left to the right and the other way round.

"This is madness!" He wanted to shout to deny going up there, but then he heard a yell from the behind.

"They are on the roof, The man in combat suit shouted and with his companion, he started his way to Alex.

The boy had no time to hesitate. He grabbed the ladder and jumped into action.

But right before he could have sat onto his seat, a strong fist grabbed his ankle. It was a soldier, probably the one he'd heard shouting.

"Let me go!" The boy yelled desperately, kicking with all the power left in his muscles, but the iron grip was too strong.

Yassen saw it from his place and said something to the pilot. The copter started to rise, pulling Alex and the guy into the air.

They were flying above the buildings of the city. Alex felt the chilly air bumping to his face. The higher they got, the colder. It made the boy more awake, but it still didn't help the loss of force in his arms, that were holding himself on the ladder.

It wasn't his own body's weight that caused the problem.

"Stop!" The man groaned under him. He was still pulling his leg down to himself.

Alex peeked at him and saw him taking a gun out of his pocket, pointing it at him.

The boy let out a little gasp and kicked with his leg frantically.

Finally he managed to hit the hand of the man, who lost his balance and dropped it, swearing. The dark object began its journey to the ground, which was already feets underneath.

"Give it up, buddy!" The one with combat clothes shouted. "You can't fight forever!"  
Then, as a new wave of wind him them, he leaned backwards and his vest moved a bit releasing a scorpion shaped tattoo.

Alex's eyes widened. Then, he saw something else.

They were getting extremely close to the top of a skyscraper. He looked down, then up.  
Yassen seemingly didn't care, he was just staring out of the window with a smile on his face.

"The building!" Alex tried to say, but from the sound of the helicopter, even he couldn't understand himself.

The man under him was glancing at him, not paying attention to the danger.

Alex looked to the massive stone wall again, imagining getting crashed to it.

The distance was getting less and less between it and him.

He put his free leg into its direction to block the force of the impact, but he knew deep inside that it would make no sense.

And then the moment arrived. But it wasn't the boy who got crashed.  
As the copter rose in the last minute, the man who was in the deepest position got jammed to the wall, letting go of Alex's ankle.

The boy was still close to the roof of the building so much, that he straightened his legs and hanging from the ladder, started to run on the concrete top.

"Whoah!" He shouted with joy.

Then, when his feet were in the air again, Yassen gave him his arm and pulled him up to him.

"Enjoyed the flight?" He asked.

"Yeah..." Alex let out a little sigh. "Thanks for the help!" He said ironically.

"Your father always told me that the best way you can learn is fighting on your own." Yassen smiled, calling back the old memory.

"Leave my father out of it!" Alex said angrily. "Even his little finger worth more than you!"

Yassen did as if he hadn't heard the comment and got to the point.

"They weren't policemen chasing us." He said coldly.

"I know." Alex replied. "The guy had a scorpion tattoo."

Yassen nodded. "We must go to Venice as fast as we can."

"Venice?" Alex asked. "Why there?"

"We have to visit some old frieds of mine." Yassen said, smiling to himself. "And also yours..."

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 **That's it! If you liked it, please drop me a review, I really appreciate them! :D**

 **Anyway, as a little spoiler -or how to call it- I can tell you that I may bring back some antagonists who were thought to be dead to the story. If you've got and guess, please let me know! :)**


	5. Chapter 5

**Hi everyone!**

 **Thank you for the favs/follows, they mean a lot to me. :D**

 **.**

 **Sorry for not updating for a while, but everything about this story just got mixed up in my mind and I needed time to rethink some parts of it...**

 **Anyway, now I am ready, so here is the next chapter, I hope you will like it! :)**

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Chapter 5

The flight to Venice was long as hell, but Alex didn't mind it. Actually, he enjoyed every minute he could spend far from the city where he nearly lost his life. Also, staring out of the window helped him forget the events of the day. Sometimes he heard Yassen mutter something to himself, but after a few minutes passed, the noises faded into one.  
Thanks to the monotonous sound and the slow shaking of the helicopter's iron structure underneath, Alex felt his eyelids getting closer and closer to each other. Although he tried hard to resist it, tiredness took over his body.

….

Alex had no idea when he had fallen asleep, but when he got conscious and peeked out of the copter, the sight of old buildings framed by blue canals appeared in his vision. As they got closer, he noticed people sitting in the famous gondolas of Venice. They had just arrived.

Yassen murmured some words into his special untraceable phone, then he turned to the boy.

"Good news." He said. "According to a source of mine, Scorpia hasn't been informed about our arrival yet. Which means that we have better chances to make it into the villa."

Alex nearly asked the man about his so mentioned _"sources"_ , but the last sentence shocked him.

"What villa? You can't be talking about that…" He gasped.

"Oh, yes," Yassen smiled. "the Ca' Vedova… or should I call it the Widow's palace? If I know well, you have quite an unforgetable experience breaking into it…"

"You must be joking! There's nothing there!" Alex protested, but Yassen grabbed the sleeve of his jacket and pulled him closer.

"That place hides more secrets than you can imagine." He whispered eerily. "And that includes the one we need."

"And what we need is…?" Alex waited for the man to carry on, but instead, Yassen let him go and turned away.

 _"He doesn't share any details… nothing…"_ Alex thought furiously.  
In his eyes, the assassin never seemed to be the most trustworthy person on Earth. What's more, the boy couldn't understand why the break-in would bring him any close to Sabina and her parents.

But the saddest thing was that he had no other choice, but to cooperate. So he kept following him blindly _– for a little time._

….

If Yassen wasn't a dream to work with, he still had a great taste for hotels.

Having checked his room for bugs, Alex threw himself into the middle of the soft, white pillows on his bed.

He just wanted to enjoy the first time that day when he could have a little rest. He yawned gratefully and stretched his limbs, causing some of the feather filled cushions fall.

Alex let out a groan as he reached for the fluffy material. He lifted the bolsters up one-by-one and put them next to himself reluctantly, but suddenly he stopped with surprise at about the fourth one.

That pillow was too heavy for the average. Frankly, he had to use both of his arms to make it move.

"What?" He muttered to himself.

Sinister thoughts emerged through his brain as he ripped the light fabric off to see the object inside.

His first guess was that it was a bomb, but then as the whole thing came visible, Alex's eyes met a box made of wood with a huge golden _S_ on it.

"Scorpia." Alex thought. He had hard time deciding whether if he wanted to open the chest, but then his curiousity won.

"There has to be a key somewhere." He wondered and looked around himself. "Maybe it's in another cushion."

He began to tear all of the mentioned apart and as the reward of his stamina, a little piece of metal landed in his hands.

The boy took a deep breath and put it into the lock. The key fitted in and with a click, the chest opened.

Alex Rider expected to see anything, from angry poisonous snakes to the picture of his beloved ones being tortured, but not what really was inside. _To make it stranger, the chest wasn't even from the feared criminal organization…_

At the top of the ordinary-looking objects, the boy noticed a letter in a colourful envelope.

"Smithers." As he read the name on it out loud, warmness filled him. He opened the envelope instantly, but to his disappointment, there were only fragments of words written on the paper in it as if the sender was in a great hurry.

.

 _Dear …,_

 _MI6 lost. Scorpia got…  
Use the gadgets, I hope they can hel…_

 _Good luck and trust no one.  
Smithers_

 _Ps.: A good gardener always talks to the flowers._

.

Alex's eyes widened.

"Seems Yassen was right, MI6 is finished… But what did Scorpia get?" He scratched the back of his head. The whole thing was a way too troublous. _Not to mention "gardener" part…_

"Is that a monthly quotation from a bad calendar?" Alex asked himself, then the shiny content left in the box caught his attention.

He took the whole case up and poured everything carefully out of it onto his bed.

He found there a pen, glasses – night vision ones, he supposed, a bar of chocolate, a tube of the well-known Zip cream, a stainless steel knife, a little Teddy bear and lipstick…

"Is that some kind of ill joke?" Alex groaned as he stared at the blood-red coloured last item.

 _"Maybe Smithers had to escape from something and he just jammed everything that got between his fingers into the chest…"_ He thought.

Desperation was the only thing that filled his mind.  
 _What if the fat, but kind friend of him wasn't even alive? What if he was the last one standing?_

His thoughts were interrupted by a knocking sound.

"The dinner is ready, Mr. Rider!" Somebody shouted from the other side of the door.

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 **So, did you like it? :)**

 **If you have any guesses about the "A good gardener always talks to the flowers." part's meaning, I would be grateful to read it.**


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